1VAQ

Crystal structure of the Mg2+-(chromomycin A3)2-d(TTGGCCAA)2 complex reveals GGCC binding specificity of the drug dimer chelated by metal ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

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Literature

Crystal structure of the [Mg2+-(chromomycin A3)2]-d(TTGGCCAA)2 complex reveals GGCC binding specificity of the drug dimer chelated by a metal ion

Hou, M.H.Robinson, H.Gao, Y.G.Wang, A.H.-J.

(2004) Nucleic Acids Res 32: 2214-2222

  • DOI: 10.1093/nar/gkh549
  • Primary Citation of Related Structures:  
    1VAQ

  • PubMed Abstract: 
  • The anticancer antibiotic chromomycin A3 (Chro) is a DNA minor groove binding drug belonging to the aureolic family. Chro likely exerts its activity by interfering with replication and transcription. Chro forms a dimer, mediated by a divalent metal ion, which binds to G/C-rich DNA ...

    The anticancer antibiotic chromomycin A3 (Chro) is a DNA minor groove binding drug belonging to the aureolic family. Chro likely exerts its activity by interfering with replication and transcription. Chro forms a dimer, mediated by a divalent metal ion, which binds to G/C-rich DNA. Herein we report the first crystal structure of Chro bound to d(TTG GCCAA)2 DNA duplex solved by multiwavelength anomalous diffraction (MAD) based on the chelated Co3+ ion. The structure of the Mg2+ complex was subsequently refined at 2.15 A resolution, which revealed two complexes of metal-coordinated dimers of Chro bound to the octamer DNA duplex in the asymmetric unit. The metal ion is octahedrally coordinated to the O1 and O9 oxygen atoms of the chromophore (CPH), and two water molecules act as the fifth and sixth ligands. The two coordinated water molecules are hydrogen bonded to O2 atoms of C5 and C13 bases. The Chro dimer binds at and significantly widens the minor groove of the GGCC sequence. The long axis of each chromophore lies along and stacks over the sugar-phosphate backbone with the two attached saccharide moieties (rings A/B and C/D/E) wrapping across the minor groove. DNA is kinked by 30 degrees and 36 degrees in the two complexes, respectively. Six G-specific hydrogen bonds between Chro and DNA provide the GGCC sequence specificity. Interestingly, DNA in concert with Chro appears to act as an effective template to catalyze the deamination of Co(NH3)6(3+), as shown by circular dichroism and crystal structure data. Our results present useful structural information for designing new anticancer drug derivatives in the future.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, 115 Taiwan.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3'A, B, C, D8synthetic construct
    Protein Feature View
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    • Reference Sequence
    Oligosaccharides

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    Entity ID: 2
    MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
    2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetateE, F, I, K2N/A Oligosaccharides Interaction
    Glycosylation Resources
    GlyTouCan:  G66610ZG
    GlyCosmos:  G66610ZG
    Entity ID: 3
    MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
    3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diolG, H, J, L3N/A Oligosaccharides Interaction
    Glycosylation Resources
    GlyTouCan:  G76712GN
    GlyCosmos:  G76712GN
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CPH (Subject of Investigation/LOI)
    Query on CPH

    Download Ideal Coordinates CCD File 
    N [auth A], O [auth B], P [auth C], R [auth D](1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
    C21 H24 O9
    AOCJXLJIUYHXRS-PKRZCTMMSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    M [auth A], Q [auth D]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.278 
    • R-Value Work: 0.235 
    • R-Value Observed: 0.235 
    • Space Group: P 65 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 42.23α = 90
    b = 42.23β = 90
    c = 246.11γ = 120
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    SOLVEphasing
    CNSrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2004-06-22
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 2.0: 2018-10-31
      Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy
    • Version 3.0: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Atomic model, Data collection, Derived calculations, Structure summary